AutoCloner

Multiple sequence alignment - TraesCS1A01G108200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS1A01G108200	chr1A	100.000	2744	0	0	1	2744	107231197	107233940	0.000000e+00	5068.0
1	TraesCS1A01G108200	chr1A	95.912	2715	104	7	1	2713	108347372	108344663	0.000000e+00	4392.0
2	TraesCS1A01G108200	chr1A	95.775	2722	99	6	1	2713	394910138	394912852	0.000000e+00	4375.0
3	TraesCS1A01G108200	chr3A	96.071	2723	90	7	1	2713	63928658	63925943	0.000000e+00	4420.0
4	TraesCS1A01G108200	chr3A	97.297	37	1	0	2708	2744	17350320	17350284	2.280000e-06	63.9
5	TraesCS1A01G108200	chr3A	100.000	34	0	0	2708	2741	731873073	731873106	2.280000e-06	63.9
6	TraesCS1A01G108200	chr6A	95.962	2724	96	4	1	2714	38581945	38584664	0.000000e+00	4409.0
7	TraesCS1A01G108200	chr4A	95.960	2723	93	7	1	2711	3626012	3628729	0.000000e+00	4403.0
8	TraesCS1A01G108200	chr4A	95.695	2718	104	9	2	2713	485049971	485047261	0.000000e+00	4359.0
9	TraesCS1A01G108200	chr4A	95.628	2722	105	4	1	2713	588239242	588236526	0.000000e+00	4355.0
10	TraesCS1A01G108200	chr4A	95.595	2724	102	8	1	2713	445774471	445771755	0.000000e+00	4349.0
11	TraesCS1A01G108200	chr2A	95.630	2723	98	7	1	2713	236855074	236857785	0.000000e+00	4349.0
12	TraesCS1A01G108200	chr7B	100.000	37	0	0	2708	2744	5041337	5041373	4.900000e-08	69.4
13	TraesCS1A01G108200	chr7B	100.000	34	0	0	2708	2741	85403384	85403417	2.280000e-06	63.9
14	TraesCS1A01G108200	chr5D	97.368	38	1	0	2707	2744	467166871	467166834	6.340000e-07	65.8
15	TraesCS1A01G108200	chr5D	97.297	37	1	0	2708	2744	175169123	175169087	2.280000e-06	63.9
16	TraesCS1A01G108200	chr5B	95.000	40	2	0	2705	2744	417642865	417642826	2.280000e-06	63.9
17	TraesCS1A01G108200	chr4D	97.297	37	1	0	2704	2740	316725676	316725640	2.280000e-06	63.9
18	TraesCS1A01G108200	chr7A	100.000	33	0	0	2708	2740	13291607	13291575	8.200000e-06	62.1

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS1A01G108200	chr1A	107231197	107233940	2743	False	5068	5068	100.000	1	2744	1	chr1A.!!$F1	2743
1	TraesCS1A01G108200	chr1A	108344663	108347372	2709	True	4392	4392	95.912	1	2713	1	chr1A.!!$R1	2712
2	TraesCS1A01G108200	chr1A	394910138	394912852	2714	False	4375	4375	95.775	1	2713	1	chr1A.!!$F2	2712
3	TraesCS1A01G108200	chr3A	63925943	63928658	2715	True	4420	4420	96.071	1	2713	1	chr3A.!!$R2	2712
4	TraesCS1A01G108200	chr6A	38581945	38584664	2719	False	4409	4409	95.962	1	2714	1	chr6A.!!$F1	2713
5	TraesCS1A01G108200	chr4A	3626012	3628729	2717	False	4403	4403	95.960	1	2711	1	chr4A.!!$F1	2710
6	TraesCS1A01G108200	chr4A	485047261	485049971	2710	True	4359	4359	95.695	2	2713	1	chr4A.!!$R2	2711
7	TraesCS1A01G108200	chr4A	588236526	588239242	2716	True	4355	4355	95.628	1	2713	1	chr4A.!!$R3	2712
8	TraesCS1A01G108200	chr4A	445771755	445774471	2716	True	4349	4349	95.595	1	2713	1	chr4A.!!$R1	2712
9	TraesCS1A01G108200	chr2A	236855074	236857785	2711	False	4349	4349	95.630	1	2713	1	chr2A.!!$F1	2712

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
849	853	0.617535	TGATCCAGGGATGACACCGT	60.618	55.0	5.35	0.0	34.6	4.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2547	2575	0.889306	GAGCACGGTCTACCAACTCT	59.111	55.0	0.0	0.0	35.14	3.24	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
160	161	2.996621	GGTCATCCGTCTTCTCAAACAG	59.003	50.000	0.00	0.00	0.00	3.16
192	193	0.879090	GAAACCAAACGGAGGCGATT	59.121	50.000	0.00	0.00	0.00	3.34
318	319	9.498176	CTGGATTATCATGTGAATCTCAACATA	57.502	33.333	16.58	0.00	33.41	2.29
518	521	9.987272	CAGCCAAATATGCATATAGTATAGCTA	57.013	33.333	19.39	0.00	0.00	3.32
567	570	3.117550	ACCTTGCCAGCATATTCCATGTA	60.118	43.478	0.00	0.00	0.00	2.29
572	575	4.202493	TGCCAGCATATTCCATGTACTGAT	60.202	41.667	0.00	0.00	0.00	2.90
697	701	4.534103	ACTCACTTATCTTCCAAGCCTTCT	59.466	41.667	0.00	0.00	0.00	2.85
823	827	1.272490	CCGAGTACTGTGTGGTGTCAT	59.728	52.381	0.00	0.00	0.00	3.06
849	853	0.617535	TGATCCAGGGATGACACCGT	60.618	55.000	5.35	0.00	34.60	4.83
868	872	2.794282	CGTAGCACAGAGATCAGACTGC	60.794	54.545	12.28	6.07	37.61	4.40
959	963	7.654116	GCTAAAAGACCTAGATCACTATTCACC	59.346	40.741	0.00	0.00	0.00	4.02
972	976	6.732487	TCACTATTCACCCTCTTCTCTTCTA	58.268	40.000	0.00	0.00	0.00	2.10
974	978	7.841729	TCACTATTCACCCTCTTCTCTTCTAAT	59.158	37.037	0.00	0.00	0.00	1.73
1130	1135	2.914695	ACCTACAACGCCACTTTACA	57.085	45.000	0.00	0.00	0.00	2.41
1210	1215	5.023452	TCACTGAGCCCATAGAGTTTTCTA	58.977	41.667	0.00	0.00	40.10	2.10
1213	1218	6.825721	CACTGAGCCCATAGAGTTTTCTATTT	59.174	38.462	0.00	0.00	42.67	1.40
1221	1226	7.040409	CCCATAGAGTTTTCTATTTATGCACCC	60.040	40.741	0.00	0.00	42.67	4.61
1251	1256	0.107017	TAGGAAAGAGCATGGCAGCC	60.107	55.000	3.66	3.66	34.23	4.85
1252	1257	1.379576	GGAAAGAGCATGGCAGCCT	60.380	57.895	14.15	0.00	34.23	4.58
1267	1272	1.130054	AGCCTACATCGCCATGGGAT	61.130	55.000	15.13	11.66	35.61	3.85
1422	1427	2.881074	CACATTCGACGACAGGAGAAT	58.119	47.619	0.00	0.00	34.06	2.40
1434	1439	0.529337	AGGAGAATCAGATGTGCGCG	60.529	55.000	0.00	0.00	36.25	6.86
1560	1565	5.152623	AGAAGAATGACGACCTGATCAAA	57.847	39.130	0.00	0.00	0.00	2.69
1647	1652	3.657634	CCCGGAAGACTACATCATCATG	58.342	50.000	0.73	0.00	35.92	3.07
1732	1737	1.071542	TCATGGAGTCTGCAACCGAAA	59.928	47.619	0.00	0.00	0.00	3.46
1768	1776	5.686753	AGACCACCTCATCAGTAGTAGTAG	58.313	45.833	0.00	0.00	0.00	2.57
1769	1777	5.192121	AGACCACCTCATCAGTAGTAGTAGT	59.808	44.000	0.00	0.00	0.00	2.73
1770	1778	6.386342	AGACCACCTCATCAGTAGTAGTAGTA	59.614	42.308	0.00	0.00	0.00	1.82
1927	1936	6.070881	CCCCCTCTATTCTTACATCTCATCTG	60.071	46.154	0.00	0.00	0.00	2.90
1930	1939	8.428063	CCCTCTATTCTTACATCTCATCTGTTT	58.572	37.037	0.00	0.00	0.00	2.83
2547	2575	2.092103	AGCAACCTTCAACAACTACCCA	60.092	45.455	0.00	0.00	0.00	4.51
2649	2677	2.574006	ACAATTCAGGAGCTCAGCAA	57.426	45.000	17.19	4.46	0.00	3.91
2714	2742	0.387202	CATGGAGGAGGTAGCTCGTG	59.613	60.000	20.88	8.30	0.00	4.35
2715	2743	0.033011	ATGGAGGAGGTAGCTCGTGT	60.033	55.000	20.88	5.87	0.00	4.49
2716	2744	0.251653	TGGAGGAGGTAGCTCGTGTT	60.252	55.000	20.88	4.43	0.00	3.32
2717	2745	0.173708	GGAGGAGGTAGCTCGTGTTG	59.826	60.000	20.88	0.00	0.00	3.33
2718	2746	0.173708	GAGGAGGTAGCTCGTGTTGG	59.826	60.000	20.88	0.00	0.00	3.77
2719	2747	1.218316	GGAGGTAGCTCGTGTTGGG	59.782	63.158	15.43	0.00	0.00	4.12
2720	2748	1.218316	GAGGTAGCTCGTGTTGGGG	59.782	63.158	6.12	0.00	0.00	4.96
2721	2749	1.229082	AGGTAGCTCGTGTTGGGGA	60.229	57.895	0.00	0.00	0.00	4.81
2722	2750	0.834687	AGGTAGCTCGTGTTGGGGAA	60.835	55.000	0.00	0.00	0.00	3.97
2723	2751	0.672711	GGTAGCTCGTGTTGGGGAAC	60.673	60.000	0.00	0.00	0.00	3.62
2724	2752	1.012486	GTAGCTCGTGTTGGGGAACG	61.012	60.000	0.00	0.00	41.11	3.95
2725	2753	1.466025	TAGCTCGTGTTGGGGAACGT	61.466	55.000	0.00	0.00	40.61	3.99
2726	2754	1.005867	GCTCGTGTTGGGGAACGTA	60.006	57.895	0.00	0.00	40.61	3.57
2727	2755	1.012486	GCTCGTGTTGGGGAACGTAG	61.012	60.000	0.00	0.00	40.61	3.51
2729	2757	1.541147	CTCGTGTTGGGGAACGTAGTA	59.459	52.381	0.00	0.00	45.00	1.82
2730	2758	1.959985	TCGTGTTGGGGAACGTAGTAA	59.040	47.619	0.00	0.00	45.00	2.24
2731	2759	2.562298	TCGTGTTGGGGAACGTAGTAAT	59.438	45.455	0.00	0.00	45.00	1.89
2732	2760	3.006752	TCGTGTTGGGGAACGTAGTAATT	59.993	43.478	0.00	0.00	45.00	1.40
2733	2761	3.747529	CGTGTTGGGGAACGTAGTAATTT	59.252	43.478	0.00	0.00	45.00	1.82
2734	2762	4.143052	CGTGTTGGGGAACGTAGTAATTTC	60.143	45.833	0.00	0.00	45.00	2.17
2735	2763	4.756135	GTGTTGGGGAACGTAGTAATTTCA	59.244	41.667	0.00	0.00	45.00	2.69
2736	2764	5.239087	GTGTTGGGGAACGTAGTAATTTCAA	59.761	40.000	0.00	0.00	45.00	2.69
2737	2765	5.826737	TGTTGGGGAACGTAGTAATTTCAAA	59.173	36.000	0.00	0.00	45.00	2.69
2738	2766	6.320672	TGTTGGGGAACGTAGTAATTTCAAAA	59.679	34.615	0.00	0.00	45.00	2.44
2739	2767	6.956202	TGGGGAACGTAGTAATTTCAAAAA	57.044	33.333	0.00	0.00	45.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
192	193	2.930950	CACTTTTCCCCACAAGACTCA	58.069	47.619	0.00	0.00	0.00	3.41
336	337	6.417635	GCATCATCATTAAACATAACCCAACG	59.582	38.462	0.00	0.00	0.00	4.10
456	458	5.782893	TGGTTACAGTTTTGCATAAAGCT	57.217	34.783	0.00	0.00	45.94	3.74
518	521	9.466497	AACACATACAGAGTAATGGAATGAAAT	57.534	29.630	0.00	0.00	0.00	2.17
536	539	2.432444	TGCTGGCAAGGTAACACATAC	58.568	47.619	0.00	0.00	41.41	2.39
589	593	7.707464	TCGTCTGAAAAGTCTACAACATTAACA	59.293	33.333	0.00	0.00	0.00	2.41
697	701	3.991773	GCCATCTAATAACGATAACCGCA	59.008	43.478	0.00	0.00	43.32	5.69
700	704	7.148457	GCTTAAGGCCATCTAATAACGATAACC	60.148	40.741	5.01	0.00	34.27	2.85
823	827	4.101585	GTGTCATCCCTGGATCAGTAATGA	59.898	45.833	0.00	0.00	32.21	2.57
849	853	2.732763	AGCAGTCTGATCTCTGTGCTA	58.267	47.619	3.32	0.00	39.44	3.49
868	872	0.888619	TGTAGCGACCAGACCTCAAG	59.111	55.000	0.00	0.00	0.00	3.02
959	963	9.889128	AAAGATGAGAAATTAGAAGAGAAGAGG	57.111	33.333	0.00	0.00	0.00	3.69
1130	1135	1.483827	TCATCCAGCGCTCTTCTTCAT	59.516	47.619	7.13	0.00	0.00	2.57
1210	1215	3.010584	AGACTCCAAGTGGGTGCATAAAT	59.989	43.478	0.00	0.00	38.11	1.40
1213	1218	1.656587	AGACTCCAAGTGGGTGCATA	58.343	50.000	0.00	0.00	38.11	3.14
1221	1226	3.259374	TGCTCTTTCCTAGACTCCAAGTG	59.741	47.826	0.00	0.00	0.00	3.16
1251	1256	0.250424	TGCATCCCATGGCGATGTAG	60.250	55.000	28.94	14.98	39.48	2.74
1252	1257	0.401356	ATGCATCCCATGGCGATGTA	59.599	50.000	28.94	27.03	39.48	2.29
1267	1272	1.405526	GCGGTAGACTTCTCCAATGCA	60.406	52.381	0.00	0.00	0.00	3.96
1422	1427	1.810853	CATGTCCGCGCACATCTGA	60.811	57.895	13.89	0.00	34.60	3.27
1434	1439	5.011943	AGCCTTCTTCAGATCTATCATGTCC	59.988	44.000	0.00	0.00	0.00	4.02
1560	1565	6.498303	GGCCTCCCATAAATATTCCAATCTTT	59.502	38.462	0.00	0.00	0.00	2.52
1732	1737	9.213777	TGATGAGGTGGTCTACTAGAAATATTT	57.786	33.333	0.00	0.00	0.00	1.40
1768	1776	9.310716	GACTACTTTATTTACATGGTGGACTAC	57.689	37.037	0.00	0.00	0.00	2.73
1769	1777	8.480501	GGACTACTTTATTTACATGGTGGACTA	58.519	37.037	0.00	0.00	0.00	2.59
1770	1778	7.336396	GGACTACTTTATTTACATGGTGGACT	58.664	38.462	0.00	0.00	0.00	3.85
1927	1936	3.444034	GGAGGCATCTGAGGGTTTAAAAC	59.556	47.826	0.00	0.00	0.00	2.43
1930	1939	1.209504	CGGAGGCATCTGAGGGTTTAA	59.790	52.381	0.00	0.00	33.17	1.52
2547	2575	0.889306	GAGCACGGTCTACCAACTCT	59.111	55.000	0.00	0.00	35.14	3.24
2649	2677	4.341487	GTCTAGGGGTAAAACATGGCTTT	58.659	43.478	0.00	0.00	0.00	3.51
2679	2707	2.694628	TCCATGGGTATGCTGAAAATGC	59.305	45.455	13.02	0.00	32.79	3.56
2714	2742	5.945466	TTGAAATTACTACGTTCCCCAAC	57.055	39.130	0.00	0.00	0.00	3.77
2715	2743	6.956202	TTTTGAAATTACTACGTTCCCCAA	57.044	33.333	0.00	0.00	0.00	4.12
2716	2744	6.956202	TTTTTGAAATTACTACGTTCCCCA	57.044	33.333	0.00	0.00	0.00	4.96

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.